ChipInfo-class: Class to represent SNP annotation for a microarray

Description Usage Arguments Fields Author(s)


This class annotates a microarray SNP chip with data for each SNP including chromosome, id, position, strand, 'rs' id, allele 1, allele 2 for each SNP of a microarray chip, in either hg18, hg19 or hg38 (build 36/37/38) coordinates. This package makes extension use of this class of annotation object for the working microarray chip, e.g, default is ImmunoChip, and you can also load your own annotation if using a different chip. The class is basically a GRanges object, modified to always have columns for A1, A2 (alleles),, and a quality control flag. The default display is tidier than GRanges, it has nice coersion to and frame data.frame and subsetting by chromosome using [[n]] has been added, in addition to normal [i,j] indexing native to GRanges. Note that with this package the first time annotation is used it might be slow, but subsequent calls should be fast. METHODS "[[", show, print, length, dim, rownames, initialize build, chip,, A1, A2, QCcode, QCcode<-, QCpass, QCfail convTo36, convTo37, convTo38 COERCION can use 'as' to convert to and from: GRanges, RangedData, data.frame

Use the 'ChipInfo()' wrapper to construct ChipInfo objects from scratch


## S4 method for signature 'ChipInfo'
initialize(.Object, ...)



An object generated from the ChipInfo class prototype, see methods:initialize


Additional arguments to initialize. None recommended.



Object of class "Rle", containing chromosomes for each range, see GRanges.


Object of class "IRanges", containing genomic start and end, see GRanges.


Object of class "Rle", containing plus or minus coding for forward or reverse strand, see GRanges.


Object of class "Seqinfo", containing chromosome listing, see GRanges.


Name, class "character", containing user description of the chip, e.g, 'immunoChip'.


Object of class "character", annotation version, e.g, hg18, hg19, hg38, etc.


Object of class "DataFrame", see GRanges, but with specific column names: A1, A2, QCcode and


Nick Cooper

humarray documentation built on Nov. 20, 2017, 1:05 a.m.